Hi Iain,
Thanks for your reply. The path for tclsh is "/usr/local/tcltkblt/bin/".
There are six files: bltsh, bltwish, tclsh, tclsh8.4, wish and wish8.4. The
tclsh
and wish are symbolic links for tclsh8.4 and wish8.4, respectively. For the
permission reason you mentioned, I have also tried this change:
sudo chown yjpeng:yjpeng -R /usr/local/tcltkblt
It does NOT work!
For better analysis, I paste my ccp4.setup file as following:
################### THIS SECTION MUST BE EDITED #####################
# CCP4_MASTER is the location of the top-level directory containing
`ccp4-<version>'
# This is usually the directory in which you ran the tar command to unpack
the
# code, and is assumed to be shared between machines at a multi-machine
site.
setenv CCP4_MASTER /home/prog/ccp4-6.0.2
setenv CCP4 $CCP4_MASTER/ccp4-6.0.2
# Check for existence of CCP4_MASTER
if (! -e $CCP4_MASTER) then
echo "********************* WARNING **********************"
echo "The directory $CCP4_MASTER"
echo "(assigned to CCP4_MASTER) does not exist."
echo "The CCP4 programs will not run correctly, and any"
echo "installation attempt will have errors or will fail."
echo "********************* WARNING **********************"
endif
# CCP4_SCR: a per-user directory for run-time-generated scratch
# files. A dedicated scratch filesystem is probably better than (/usr)/tmp
# BINSORT_SCR: a scratch directory for binsort's use; normally same as
CCP4_SCR
setenv CCP4_SCR /data/tmp
# check to see if this exists and if not try to make it
if (! -e $CCP4_SCR) mkdir $CCP4_SCR
if (! -e $CCP4_SCR) \
echo "Unable to make CCP4_SCR. CCP4 progs will not run correctly."
setenv BINSORT_SCR $CCP4_SCR
### CCP4i setup - you may need to edit CCP4I_TCLTK ###
# CCP4I_TOP - the top directory of the interface
setenv CCP4I_TOP ${CCP4}/ccp4i
# CCP4I_TCLTK - directory containing tclsh,wish and bltwish executables
# as used in $CCP4I_TOP/bin/ccp4i,ccp4ish,loggraph
# For 'standard' installations this is /usr/local/bin
# but note the SGI distributed version of Tcl/Tk is not
# appropriate version
setenv CCP4I_TCLTK /usr/local/tcltkblt/bin
# CCP4I_HELP - directory contain ccp4i help - default is $CCP4I_TOP/help
setenv CCP4I_HELP ${CCP4I_TOP}/help
### Optional - setting http_proxy environment
# The commented out 'setenv' line below may have to be declared to download
# and edit protein sequences using the new "Import/Edit Protein Sequences"
# (This may also be required for remote job submission in arp/warp.)
# task. If so, uncomment this line and replace the example proxy URL with
your
# relevant URL
#setenv HTTP_PROXY wwwblah.blah.ac.uk:xxxx/blah.blah
################### NOVICE USERS STOP HERE #####################
################### OPTIONS TO CUSTOMISE CCP4 #####################
# By default, CCP4 directories are appended to the end of paths (PATH,
# LD_LIBRARY_PATH, and DYLD_LIBRARY_PATH). If ccp4_first_in_path is set
# to 1, then they will be prepended to the beginning of paths.
# When deciding local policy, bear in mind the possible existence of
# other CCP4 installations, and the possibility of non-CCP4 programs
# with conflicting names.
set ccp4_first_in_path = 1
# The commented-out switch statement below provides an example of how
# to use this file for several machines/architectures sharing $CCP4_MASTER.
# If necessary, uncomment and edit this. Otherwise, if you're only
supporting
# a single system alter the uncommented part as necessary.
#
# The significance of the environment variables is as follows:
# CBIN: location of the executables -- must be on your path (see below);
# CLIB: location of (binary) library files such as libccp4.a and
libccp4.so;
# MANPATH: set this if your system's `man' looks at such an environment
# variable to determine where to look for man pages. By adding
# $CCP4/man to the normal path you get the CCP4 man pages
# with keyword searching as system ones.
# MCTYPE: used for LAUE make -- see LAUE documentation
# CCP4_BROWSER: set this if you intend to use the html documentation
# (recommended). It should have the path and name of a html browser eg
# /usr/bin/X11/netscape or /usr/local/bin/lynx. The browser will be
# started with the alias ccp4help and will open the file
# $CHTML/INDEX.html.
# switch (`hostname`) # edit this switch statement if used
# # for multiple systems
# case 'foo':
setenv CBIN $CCP4/bin
setenv CLIB $CCP4/lib
setenv CCP4_BROWSER firefox
if (${?MANPATH}) then
if ($ccp4_first_in_path) then
setenv MANPATH ${CCP4}/man:${MANPATH}
else
setenv MANPATH ${MANPATH}:${CCP4}/man
endif
else
if ($ccp4_first_in_path) then
setenv MANPATH ${CCP4}/man:/usr/share/man
else
setenv MANPATH /usr/share/man:${CCP4}/man
endif
endif
setenv MCTYPE unix # (only for Laue)
# breaksw
# default:
# echo "CCP4 not implemented on this system"
# exit 1
# breaksw
# endsw
switch (`uname`)
case 'Darwin':
limit stacksize 65536
breaksw
default:
breaksw
endsw
# The following are for all systems
setenv CCP4_LIB $CLIB
setenv CCP4_BIN $CBIN
# CLASSPATH for Java
if (${?CLASSPATH}) then
if ($ccp4_first_in_path) then
setenv CLASSPATH ${CBIN}:${CLASSPATH}
else
setenv CLASSPATH ${CLASSPATH}:${CBIN}
endif
else
if ($ccp4_first_in_path) then
setenv CLASSPATH ${CBIN}:.
else
setenv CLASSPATH .:${CBIN}
endif
endif
### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ###
setenv PLOT_COMMAND 'lp -s -dmicrolaser'
setenv PRINT_COMMAND 'lp -s -denscript'
# HARVESTHOME specifies location of harvesting files (defaults to $HOME)
#setenv HARVESTHOME
### CCP4_OPEN ###
# CCP4_OPEN may be set to 'UNKNOWN' to stop open failures for files opened
# as NEW that already exist. Novices should use 'NEW' to avoid inadvertant
# over-writing of existing files, which is then treated as a fatal error.
setenv CCP4_OPEN UNKNOWN
### BINSORT_MEM ###
# BINSORT_MEM is workspace used by the binsort program. In principle this
# value is machine-dependent. It may benefit from being enlarged, but
values
# higher than 2M have been reported to cause excessive paging on some
systems.
# You might like to experiment with a program such as fft with different
# values -- 102400 (bytes) is the default. csh's `time' command can tell
you
# about paging.
#
# setenv BINSORT_MEM 8388608
# LD_LIBRARY_PATH specifies where to find dynamic libraries (e.g.
libccp4.so)
# at runtime
if (${?LD_LIBRARY_PATH}) then
if ($ccp4_first_in_path) then
setenv LD_LIBRARY_PATH ${CLIB}:${LD_LIBRARY_PATH}:${CCP4}/extralib
else
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${CLIB}:${CCP4}/extralib
endif
else
setenv LD_LIBRARY_PATH ${CLIB}:${CCP4}/extralib
endif
# DYLD_LIBRARY_PATH specifies where to find dynamic libraries (e.g.
libccp4.dylib)
# at runtime (used on Mac OS X)
if (${?DYLD_LIBRARY_PATH}) then
if ($ccp4_first_in_path) then
setenv DYLD_LIBRARY_PATH ${CLIB}:${CCP4}/extralib:${DYLD_LIBRARY_PATH}
else
setenv DYLD_LIBRARY_PATH ${DYLD_LIBRARY_PATH}:${CLIB}:${CCP4}/extralib
endif
else
setenv DYLD_LIBRARY_PATH ${CLIB}:${CCP4}/extralib
endif
### XAPPLRESDIR ###
# If you want to use xloggraph/xplot84driver, you need to get the
application
# defaults picked up somehow. As distributed, the file can't just live in
an
# application defaults directory since it requires reading by xrdb to sort
out
# the differences for monochrome displays. At Daresbury a version of the
file
# assuming a monochrome display is kept in the directory
# $CCP4_LIB/X11/app-defaults and this is picked up through the
# XUSERFILESEARCHPATH environment variable. That means you only see black
and
# white on a colour display. Alternatively you might make sure that it is
# read by xrdb on startup of the X Windows system or delegate the
# responsibility to users to run it. There are disadvantages to putting an
# invocation of xrdb in here, one being that the correct value of DISPLAY
may
# not be set at the time this file is read. Thus edit this part as
# appropriate. (SunOS will normally want to use /usr/openwin or
$OPENWINHOME
# instead of /usr; others may want /usr/local/lib or somw such):
if ($?XUSERFILESEARCHPATH) then
setenv XUSERFILESEARCHPATH
$CCP4_LIB/X11/app-defaults/%N:$XUSERFILESEARCHPATH
else
setenv XUSERFILESEARCHPATH
$CCP4_LIB/X11/app-defaults/%N:/usr/lib/X11/app-defaults
endif
### TRAPPFE ###
# TRAPFPE is set to ensure (in collaboration with -lfpe) an abort on
floating
# point exceptions under IRIX. It shouldn't cause harm on other systems,
but
# edit this to comment it out if necessary.
setenv TRAP_FPE "OVERFL=ABORT; DIVZERO=ABORT; INVALID=ABORT"
# The following can be used to put a message of the day to announce news
about
# CCP4 or whatever to CCP4 users. You might also want to edit this part to
# have machine-specific messages dependent on `hostname`.
if (-e $CCP4/include/ccp4.msg) cat $CCP4/include/ccp4.msg
################### EXPERIENCED USERS STOP HERE #####################
Thanks very much.
Best regards,
Yingjie
On Tue, Sep 30, 2008 at 10:59 AM, Iain Kerr <[EMAIL PROTECTED]> wrote:
> Hello Yingjie
>
> Tclsh handles the starting and running of jobs, so it must be a problem
> with this. If you are able to startup the GUI then your path is correct is
> ccp4.setup..where are the bltwish (wish) and tclsh /usr/local/bin ?
>
> If the tclsh executable is called something like "tclsh8.4" then CCP4i will
> not recognise it..you have to make a symbolic link to the executable, in the
> same directory, as below:
>
> ln -s tclsh8.4 tclsh (or the other way round, check)..also make sure you
> have read (and possibly execute) permission for this directory and the files
> within.
>
> HTH,
> Iain
>
> Yingjie Peng wrote:
>
>> Dear friends,
>> I have installed the latest version of CCP4i under Fedora 9 on my laptop
>> HP Compaq 6515b (two processors). The system
>> setup was done and the CCP4i interface can run normally. But if I submit a
>> job, it displayes "STARTING" the job in the job window
>> and will NOT actually run the job. Also I can NOT kill the job with its
>> status as STARTING.
>> I have checked my Tcl/tk is version 8.4 and the CCP4I_TCLTK environment
>> variable is pointed to the right directory containing
>> tclsh, bltwish and other files.
>> Is there any suggestion on how to solve this problem? Thank you very much
>> in advance.
>> Best wishes,
>> Yingjie
>> Yingjie PENG, Ph.D. student
>> Structural Biology Group
>> Shanghai Institute of Biochemistry and Cell Biology (SIBCB)
>> Shanghai Institute of Biological Sciences (SIBS)
>> Chinese Academy of Sciences (CAS)
>> 320 Yue Yang Road, Shanghai 200031
>> P. R. China
>> 86-21-54921117
>> Email: [EMAIL PROTECTED]
>> ------------------------------------------------------------------------
>>
>>
>> No virus found in this incoming message.
>> Checked by AVG - http://www.avg.com Version: 8.0.173 / Virus Database:
>> 270.7.5/1698 - Release Date: 9/29/2008 7:25 PM
>>
>>
>>
>
